Magnesium in PDB 4tmz: Translation Initiation Factor EIF5B (517-858) From C. Thermophilum, Bound to Gtpgammas and Potassium

The structure of Translation Initiation Factor EIF5B (517-858) From C. Thermophilum, Bound to Gtpgammas and Potassium, PDB code: 4tmz was solved by B.Kuhle, F.Ficner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.68 / 2.28
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	116.130, 116.130, 120.270, 90.00, 90.00, 90.00
R / Rfree (%)	20 / 23.9

The structure of Translation Initiation Factor EIF5B (517-858) From C. Thermophilum, Bound to Gtpgammas and Potassium also contains other interesting chemical elements:

Potassium	(K)	2 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Magnesium atom in the Translation Initiation Factor EIF5B (517-858) From C. Thermophilum, Bound to Gtpgammas and Potassium (pdb code 4tmz). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Translation Initiation Factor EIF5B (517-858) From C. Thermophilum, Bound to Gtpgammas and Potassium, PDB code: 4tmz:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Translation Initiation Factor EIF5B (517-858) From C. Thermophilum, Bound to Gtpgammas and Potassium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Translation Initiation Factor EIF5B (517-858) From C. Thermophilum, Bound to Gtpgammas and Potassium within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg902 b:34.7 occ:1.00 O1B B:GSP901 2.0 30.2 1.0 OG1 B:THR537 2.1 30.9 1.0 O B:HOH1013 2.1 35.1 1.0 O3G B:GSP901 2.1 33.8 1.0 O B:HOH1014 2.2 32.9 1.0 OG1 B:THR557 2.2 34.9 1.0 CB B:THR537 3.1 33.3 1.0 CB B:THR557 3.2 35.4 1.0 PB B:GSP901 3.2 33.3 1.0 PG B:GSP901 3.3 36.8 1.0 O3B B:GSP901 3.4 28.9 1.0 N B:THR537 3.9 33.7 1.0 OE2 B:GLU552 4.0 35.6 1.0 CG2 B:THR557 4.1 34.6 1.0 OE1 B:GLU552 4.1 38.8 1.0 CA B:THR537 4.1 36.8 1.0 OD2 B:ASP594 4.2 38.7 1.0 O1A B:GSP901 4.2 32.5 1.0 CG2 B:THR537 4.2 32.3 1.0 O2B B:GSP901 4.2 34.7 1.0 O3A B:GSP901 4.3 42.2 1.0 CA B:THR557 4.3 36.3 1.0 N B:THR557 4.4 38.1 1.0 OD1 B:ASP594 4.4 35.1 1.0 S1G B:GSP901 4.4 33.8 1.0 CD B:GLU552 4.5 36.5 1.0 PA B:GSP901 4.5 38.0 1.0 O2G B:GSP901 4.5 33.6 1.0 O2A B:GSP901 4.5 35.6 1.0 CE B:LYS536 4.6 31.0 1.0 O B:THR595 4.6 31.2 1.0 CG B:ASP594 4.7 36.6 1.0 CB B:LYS536 4.8 31.9 1.0 NZ B:LYS536 5.0 28.2 1.0

Magnesium binding site 2 out of 2 in the Translation Initiation Factor EIF5B (517-858) From C. Thermophilum, Bound to Gtpgammas and Potassium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Translation Initiation Factor EIF5B (517-858) From C. Thermophilum, Bound to Gtpgammas and Potassium within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg902 b:48.9 occ:1.00 O3G A:GSP901 2.0 38.9 1.0 OG1 A:THR537 2.0 44.9 1.0 OG1 A:THR557 2.1 37.5 1.0 O2B A:GSP901 2.1 34.9 1.0 O A:HOH1007 2.1 47.7 1.0 O A:HOH1006 2.1 42.6 1.0 CB A:THR557 3.1 38.7 1.0 CB A:THR537 3.1 49.0 1.0 PB A:GSP901 3.3 41.9 1.0 PG A:GSP901 3.3 46.1 1.0 O3B A:GSP901 3.6 40.2 1.0 N A:THR537 3.9 46.6 1.0 CG2 A:THR557 4.0 39.4 1.0 OE1 A:GLU552 4.0 51.6 1.0 OE2 A:GLU552 4.0 48.1 1.0 OD2 A:ASP594 4.0 48.5 1.0 CA A:THR537 4.1 47.8 1.0 CG2 A:THR537 4.2 48.6 1.0 CA A:THR557 4.2 42.2 1.0 O1B A:GSP901 4.3 46.4 1.0 O2A A:GSP901 4.3 47.8 1.0 N A:THR557 4.3 45.7 1.0 OD1 A:ASP594 4.3 48.1 1.0 S1G A:GSP901 4.4 44.4 1.0 CD A:GLU552 4.4 49.1 1.0 O3A A:GSP901 4.5 51.6 1.0 CG A:ASP594 4.5 48.0 1.0 O2G A:GSP901 4.5 40.0 1.0 O A:THR595 4.6 38.4 1.0 CE A:LYS536 4.6 44.3 1.0 PA A:GSP901 4.7 47.3 1.0 O1A A:GSP901 4.7 45.4 1.0 CB A:LYS536 4.8 43.5 1.0

B.Kuhle, R.Ficner. A Monovalent Cation Acts As Structural and Catalytic Cofactor in Translational Gtpases. Embo J. 2014.
ISSN: ESSN 1460-2075
PubMed: 25225612
DOI: 10.15252/EMBJ.201488517